-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_1-193457

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_57845-T1
Valid prediction for snap_scaffold_27-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_57829-T1
Valid prediction for snap_scaffold_27-snap.22-T1
Valid prediction for snap_scaffold_27-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_57840-T1
Valid prediction for GlimmerHMM_glimmerT_57837-T1
Valid prediction for snap_scaffold_27-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_57831-T1
Valid prediction for snap_scaffold_27-snap.15-T1
Valid prediction for GeneMark_model.100713_t
Valid prediction for GeneMark_model.100701_t
Valid prediction for GlimmerHMM_glimmerT_57835-T1
Valid prediction for snap_scaffold_27-snap.35-T1
Valid prediction for GeneMark_model.100695_t
Valid prediction for snap_scaffold_27-snap.16-T1
Valid prediction for snap_scaffold_27-snap.32-T1
Valid prediction for GeneMark_model.100699_t
Valid prediction for Augustus_model.g38524.t1
Valid prediction for GeneMark_model.100718_t
Valid prediction for snap_scaffold_27-snap.36-T1
Valid prediction for snap_scaffold_27-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_57827-T1
Valid prediction for GeneMark_model.100707_t
Valid prediction for snap_scaffold_27-snap.21-T1
Valid prediction for Augustus_model.g38514.t1
Valid prediction for GlimmerHMM_glimmerT_57830-T1
Valid prediction for GlimmerHMM_glimmerT_57825-T1
Valid prediction for GeneMark_model.100712_t
Valid prediction for Augustus_model.g38525.t1
Valid prediction for Augustus_model.g38510.t1
Valid prediction for GlimmerHMM_glimmerT_57842-T1
Valid prediction for snap_scaffold_27-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_57824-T1
add_exon() Sorry, GlimmerHMM_glimmerT_57824-T1 1410-1581-terminal-1 is invalid.
Valid prediction for snap_scaffold_27-snap.2-T1
Valid prediction for GeneMark_model.100693_t
Valid prediction for snap_scaffold_27-snap.37-T1
Couldn't classify 1426, 1529
Sorry, prediction GeneMark_model.100692_t fails validation.
(GTG)	 AG	1426-1529	GT	AGG
(GCC)	 AG	2491-2512	GT	AGG
(CAG)	 AG	2682-2885	CC	GAC
-recovered GeneMark_model.100692_t, terminal, 2682, 2885
-recovered GeneMark_model.100692_t, internal, 1426, 1529
-recovered GeneMark_model.100692_t, internal, 2491, 2512
Valid prediction for GeneMark_model.100703_t
Valid prediction for GlimmerHMM_glimmerT_57848-T1
Valid prediction for Augustus_model.g38512.t1
Valid prediction for GlimmerHMM_glimmerT_57826-T1
Valid prediction for Augustus_model.g38513.t1
Valid prediction for Augustus_model.g38531.t1
Valid prediction for GeneMark_model.100706_t
Valid prediction for snap_scaffold_27-snap.4-T1
Valid prediction for Augustus_model.g38519.t1
Valid prediction for GlimmerHMM_glimmerT_57844-T1
Valid prediction for Augustus_model.g38526.t1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for Augustus_model.g38530.t1
Couldn't classify 139476, 139555
Sorry, prediction pasa_asmbl_36583.p1 fails validation.
(AAG)	 TG	139476-139555	GT	AGG
(TGG)	 AG	139643-139854	GT	GGG
(GTA)	 AG	140252-140375	GT	AGG
(GAA)	 AG	141079-141102	GT	GGG
(GTC)	 AG	141546-141766	GT	CTG
(TGT)	 AG	142135-142311	GT	GAG
(ATT)	 AG	142539-142718	GT	GGG
(TGG)	 AG	143405-143518	GT	AGG
(GCT)	 AG	144603-144799	TG	AAT
add_exon() Sorry, pasa_asmbl_36583.p1 142135-142311-terminal-1 is invalid.
-recovered pasa_asmbl_36583.p1, terminal, 142135, 142311
add_exon() Sorry, pasa_asmbl_36583.p1 143405-143518-terminal-1 is invalid.
-recovered pasa_asmbl_36583.p1, terminal, 143405, 143518
-recovered pasa_asmbl_36583.p1, terminal, 144603, 144799
-recovered pasa_asmbl_36583.p1, internal, 139643, 139854
-recovered pasa_asmbl_36583.p1, internal, 140252, 140375
-recovered pasa_asmbl_36583.p1, internal, 141079, 141102
-recovered pasa_asmbl_36583.p1, internal, 141546, 141766
-recovered pasa_asmbl_36583.p1, internal, 142135, 142311
-recovered pasa_asmbl_36583.p1, internal, 142539, 142718
-recovered pasa_asmbl_36583.p1, internal, 143405, 143518
Valid prediction for GeneMark_model.100696_t
Valid prediction for Augustus_model.g38511.t1
Valid prediction for snap_scaffold_27-snap.5-T1
Valid prediction for Augustus_model.g38534.t1
Valid prediction for Augustus_model.g38532.t1
Valid prediction for snap_scaffold_27-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_57843-T1
Valid prediction for HiQ_model.g38527.t1
Valid prediction for pasa_asmbl_36602.p1
Valid prediction for GeneMark_model.100709_t
Valid prediction for snap_scaffold_27-snap.30-T1
Valid prediction for GeneMark_model.100698_t
Valid prediction for HiQ_model.g38516.t1
Valid prediction for CodingQuarry_transcript_41641-T1
Valid prediction for GeneMark_model.100722_t
Couldn't classify 150600, 151137
Sorry, prediction pasa_asmbl_36580.p1 fails validation.
(AGT)	 CC	150600-151137	GT	AGG
(TGT)	 AG	151364-151684	GT	GGG
(ATG)	 AG	154516-154538	CT	AAC
-recovered pasa_asmbl_36580.p1, terminal, 154516, 154538
-recovered pasa_asmbl_36580.p1, internal, 151364, 151684
Valid prediction for GeneMark_model.100720_t
Valid prediction for GeneMark_model.100705_t
Valid prediction for GeneMark_model.100708_t
Valid prediction for snap_scaffold_27-snap.8-T1
Valid prediction for Augustus_model.g38520.t1
Valid prediction for GlimmerHMM_glimmerT_57841-T1
Valid prediction for snap_scaffold_27-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_57833-T1
Valid prediction for GlimmerHMM_glimmerT_57834-T1
Valid prediction for snap_scaffold_27-snap.3-T1
Valid prediction for Augustus_model.g38518.t1
Valid prediction for GlimmerHMM_glimmerT_57839-T1
Valid prediction for GeneMark_model.100719_t
Valid prediction for snap_scaffold_27-snap.14-T1
Valid prediction for snap_scaffold_27-snap.17-T1
Valid prediction for GeneMark_model.100710_t
Valid prediction for snap_scaffold_27-snap.29-T1
Valid prediction for GeneMark_model.100721_t
Valid prediction for GeneMark_model.100702_t
Valid prediction for snap_scaffold_27-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_57838-T1
Valid prediction for Augustus_model.g38533.t1
Valid prediction for snap_scaffold_27-snap.28-T1
Valid prediction for Augustus_model.g38528.t1
Valid prediction for GeneMark_model.100711_t
Valid prediction for Augustus_model.g38522.t1
Valid prediction for Augustus_model.g38517.t1
Valid prediction for snap_scaffold_27-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_57832-T1
Valid prediction for snap_scaffold_27-snap.31-T1
Valid prediction for GeneMark_model.100694_t
Valid prediction for snap_scaffold_27-snap.20-T1
Valid prediction for Augustus_model.g38521.t1
Valid prediction for snap_scaffold_27-snap.6-T1
Valid prediction for snap_scaffold_27-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_57846-T1
Valid prediction for GlimmerHMM_glimmerT_57851-T1
Valid prediction for GeneMark_model.100697_t
Couldn't classify 132487, 132663
Couldn't classify 133571, 133767
Sorry, prediction pasa_asmbl_36584.p1 fails validation.
(AAC)	 TA	132487-132663	GT	AGG
(ATC)	 AG	133125-133233	GT	CGG
(TCT)	 AG	133571-133767	AT	AGA
-recovered pasa_asmbl_36584.p1, internal, 133125, 133233
Valid prediction for snap_scaffold_27-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_57849-T1
Valid prediction for pasa_asmbl_36588.p1
Valid prediction for snap_scaffold_27-snap.10-T1
Valid prediction for snap_scaffold_27-snap.25-T1
Valid prediction for snap_scaffold_27-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_57847-T1
Valid prediction for GlimmerHMM_glimmerT_57828-T1
Valid prediction for GeneMark_model.100714_t
Valid prediction for CodingQuarry_transcript_41642-T1
Valid prediction for snap_scaffold_27-snap.19-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_36600.p1
Valid prediction for snap_scaffold_27-snap.9-T1
Couldn't classify 127367, 127525
Couldn't classify 128393, 128530
Sorry, prediction pasa_asmbl_36585.p1 fails validation.
(CTG)	 AG	127367-127525	GT	AGG
(TTT)	 AG	128393-128530	CA	GAC
-recovered pasa_asmbl_36585.p1, internal, 127367, 127525
Valid prediction for GeneMark_model.100716_t
Valid prediction for GeneMark_model.100715_t
Valid prediction for GlimmerHMM_glimmerT_57836-T1
Valid prediction for GlimmerHMM_glimmerT_57850-T1
Couldn't classify 45594, 45731
Couldn't classify 47533, 47801
Sorry, prediction pasa_asmbl_36595.p1 fails validation.
(CAG)	 AT	45594-45731	GT	AGG
(GGC)	 AG	46192-46292	GT	AGG
(GTC)	 AG	46425-46499	GT	ACG
(GTT)	 AG	46656-46738	GT	AGG
(GTT)	 AG	47533-47801	CC	CCC
add_exon() Sorry, pasa_asmbl_36595.p1 46656-46738-terminal-2 is invalid.
-recovered pasa_asmbl_36595.p1, terminal, 46656, 46738
-recovered pasa_asmbl_36595.p1, internal, 46192, 46292
-recovered pasa_asmbl_36595.p1, internal, 46425, 46499
-recovered pasa_asmbl_36595.p1, internal, 46656, 46738
Valid prediction for snap_scaffold_27-snap.13-T1
Valid prediction for Augustus_model.g38515.t1
Valid prediction for GeneMark_model.100700_t
Valid prediction for GeneMark_model.100717_t
Valid prediction for Augustus_model.g38529.t1
Valid prediction for snap_scaffold_27-snap.27-T1
Valid prediction for Augustus_model.g38523.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 113781, rend_intergenic: 110498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182872, rend_intergenic: 178083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193457
-exon list size: 471


building trellis

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31.9    
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32.6    
32.8    
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34.9    
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36.8    
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38.3    
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38.7    
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84.4    
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86.0    
86.3    
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87.3    
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87.9    
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90.3    
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90.9    
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91.8    
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92.8    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 113781, rend_intergenic: 110498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182872, rend_intergenic: 178083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support